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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 9
ttgactgttcttatccaattggtgcgtaaaatcc--ccagatgtgtttgtttat-ccagtgagagtgtgatgcttcttagctaatttg-ttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
    || || ||  |  |||||   |||   | |     |   ||  |  |  | |  |||    |   ||   || || || ||||| ||||| ||||| |||||| || || || |||||||| |||||||||||||||||||| ||||| ||||| ||||||||  ||||| | |||| ||||| ||||||||| ||||||
--tgctattttttcc--attggctggtaccgttcagtgtgtactgcctactactgctggtgtagctacaatcggtcatatctgatttgcttttatatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAGAGGATATGCAGATGCGGCTCAA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtt-tatccagtgagag--tgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
     |||   | |  |  ||    |||   |||   |   ||  |  | |  |  |||      | ||   |   | | ||||||||||||| ||||| |||||| || ||||| |||||||| || ||||||||||||||||| ||||| ||||| || |||||  ||||| | |||||||| | ||| ||||||||||||
---tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 7
ttgactgttcttatccaattggtgc-gtaaaatcc-ccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
 || || || ||| |  |   || | ||  | |   | |  |    ||| || || ||      ||  |    |  || || ||||| |||| || |  |||||| || ||||| |||||||  |||||||||||||||||||| ||||| ||||| ||||||||  ||||| | |||||||||| ||| ||||||||||||
-tgtctatttttagctgaccagtactgtccagtgtactaactactattgcttgtctagccttc-tgctaccacttatatctgatttgctttatatcgttcagTGATGGAGCTGCTGCATTAGCTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAAAGGATATGCTGATGCAGCTCAA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatgg---aacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
     |||   | |  || |      |   ||     ||  |  ||    ||  |||||    |   || || |||   || |     | |       |||||||| |||||||| ||| |||| |||||||||||  |||||||||   | ||||| || ||||||||||||  |||||  |||| ||| ||||| ||||| 
-aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacatt-agtgatta-gccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86867692|gb|CI342669.1|CI342669
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|27410210|gb|CA923280.1|CA923280
EST:     ACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: ACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|29640958|gb|CB645965.1|CB645965
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|86498219|gb|CI140852.1|CI140852
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|87020189|gb|CI259259.1|CI259259
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|33678061|gb|CF306300.1|CF306300
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|33683367|gb|CF311606.1|CF311606
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|88906443|gb|CI375515.1|CI375515
EST:     TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
EST: gi|5607308|gb|AU075980.1|AU075980
EST:     GGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG                         TGACGGT-CTGCCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAAC
genomic: GGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTG-CCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
                              agctaat  putative branch site (score: 3)
                                 taatttgttttacat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA